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RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310. Epub 2010 Aug 10.

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

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Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.


It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N(2)) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at:

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